You know what? I'm going to reserve judgement on that one for now, until I fight players all kitted out with these.
So far, using non-rep characters in pvp is still perfectly viable, in my experience - once they fixed the bogus shield boost that one of these t4's gave. Even when I am thoroughly outgeared, it's mostly the elite fleet shields that flatline my attacks.
Sure, they're more unstrippable bonuses that you get without sacrificing for elsewhere, but they're not massive, per se. They look like the kind of thing that might, just might, tip the balance in situations where 2 exactly identically skilled captains fly exactly identically outfitted identical ships - how often does that happen anyway?
PvP isn't as much an issue, at least not yet. Those of us currently playing will all keep up with the rep systems and all be on even playing field. The shield ignoring passives from Omega and Nukara reps can only help with the absurd levels of shield damage resist we're seeing. New players might have a problem as more and more reps come online. It'll just be crazy trying to grind them all out at once.
The bigger issue I think is PvE, honestly. Just look at how even half assed PUGs can faceroll an ESTF with all their top end gear and rep powers. ISE is barely even challenging anymore. Even if somebody pops a generator early, we still melt the transformer faster than the spheres can get there. Also, look at how fast the CE is going down. It took people a few days to get used to the mission, but now it's like child's play. If we keep having this power creep, even the game's hardest content is going to be way too easy.